Theory - Conformations
There are two closely related and often confusing concepts about molecular 3D structures: conformations and conformers. A conformer of a molecule is a local or global energy minimum structure, while a conformation is any 3D structure of a molecule, which may or may not be an energy minimum. In most applications, such as pharmacophore modeling, the low energy conformations of molecules are used. In Discovery Studio, you can use the Search Small Molecule Conformations tools and the Generate Conformations protocol to generate conformations. The tool panel provides an easy and intuitive way for quick conformation generation and visual inspection of the conformation models. The protocol, on the other hand, provides more advanced controls for conformation search, such as energy minimization in solvation.
Six conformation search methods are available in the Generate Conformations protocol:
- FAST - Quickly provides diverse low-energy conformations. For details, see FAST conformation generation.
- BEST - Ensures the best coverage of conformational space (requires more CPU time). For details, see BEST conformation generation.
- CAESAR - Very quickly provides conformations by sampling torsions. For details, see CAESAR conformation generation.
- Systematic Search - Systematically search on torsion grids of user defined rotatable bonds.
- Random Search - Randomly change torsion angles of user selected rotatable bonds
- Boltzmann Jump - A stochastic search method where random changes in the specified torsion angles are accepted or rejected according to the Metropolis selection criterion.
Note. For details about Systematic, Random, and Boltzmann jump methods, see Torsion search methods.
Search Small Molecule Conformations tools
The Search Small Molecule Conformations tool panel provides a quick way to generate conformations by searching the torsion space of user-defined rotatable bonds.
To display the Search Small Molecule Conformations tool panel
Choose the View | Tool Panels | Search Small Molecule Conformations command from the menu bar.
Conformation Search Setup
Find Rotatable Bonds: Adds Rotatable Bond Attributes to the selected bonds for each molecule, or all rotatable bonds if nothing is selected. During the conformation generation, the torsions will only be varied for bonds that have these attributes.
Conformation Method: Allows you to select the conformation generation method to use: Systematic, Random, or Boltzmann Jump. For details about Systematic, Random, and Boltzmann jump methods, see Torsion search methods.
Energy Threshold: Allows you to select the maximum energy threshold for the final conformations. The value can also be changed using the Energy Threshold property found in the Molecule tab of the Data Table View.
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